SMTL ID : 5w97.1

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Serial Femtosecond X-Ray Crystallography at Room Temperature

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

4 x HEA: HEME-A(Non-covalent)

HEA.1: 35 residues within 4Å: Chain A: G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:T.31, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.425 pi-Cation interactions: A:H.378 Metal complexes: A:H.61, A:H.378 HEA.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CMO.9 35 PLIP interactions: 30 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:L.353, A:I.356, A:L.358, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, A:L.381, B:I.34, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:D.369, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438 Metal complexes: A:H.376, CMO.9 HEA.30: 30 residues within 4Å: Chain N: M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 36 PLIP interactions: 36 interactions with chain N, Hydrophobic interactions: N:T.31, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:L.381, N:L.381, N:V.386, N:V.386, N:F.393, N:T.424, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:W.126, N:Y.371, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:H.378, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.31: 32 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain O: I.34, P.69, I.72, L.73 Ligands: CMO.37 34 PLIP interactions: 30 interactions with chain N, 3 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:T.316, N:T.349, N:L.353, N:I.356, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381, N:L.381, O:I.34, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:T.316, N:D.369, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, CMO.37

2 x CU: COPPER (II) ION(Non-covalent)

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.9 CU.32: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CMO.37 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, CMO.37

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.9, H2O.9, H2O.11 MG.33: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: D.173, E.198 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.39, H2O.39

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.45 Water bridges: A:Q.43 NA.34: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40, N:S.441, N:D.442

8 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.6: 13 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 11 PLIP interactions: 4 interactions with chain M, 3 interactions with chain D, 3 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: M:P.12, M:P.12, M:A.16, M:L.19, D:T.80, D:A.84, D:F.87, A:T.408, A:W.409, A:W.409, K:F.9 PGV.7: 24 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152 Chain C: H.9, V.11, A.24, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90 Ligands: PEK.14, PGV.15 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:A.24, C:L.31, C:W.57, C:W.57, C:W.58, C:F.86, C:E.90, A:L.152 Hydrogen bonds: C:H.9, C:H.71, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.15: 21 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, H.71, M.83, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.7, CDL.17 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:T.66, C:R.221, C:F.233, C:G.234 Water bridges: C:R.221, C:H.231, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.16: 12 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain H: N.22 Chain P: W.258 Chain T: A.1, S.2 Ligands: CHD.13, PEK.21 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 3 interactions with chain H Water bridges: A:D.298, A:D.298, H:N.22 Hydrophobic interactions: C:T.95, C:W.99, C:W.99 Hydrogen bonds: H:N.22, H:N.24 PGV.26: 9 residues within 4Å: Chain C: W.258, W.259 Chain G: A.1 Chain P: T.95, W.99, H.103, L.106 Ligands: CDL.24, CHD.41 8 PLIP interactions: 1 interactions with chain N, 4 interactions with chain C, 3 interactions with chain P Hydrogen bonds: N:D.298 Hydrophobic interactions: C:W.258, C:W.258, C:W.258, C:W.259, P:W.99, P:W.99, P:W.99 PGV.36: 11 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: A.3, K.4, Q.15 8 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain N, 2 interactions with chain Z, 2 interactions with chain X Hydrophobic interactions: Q:A.84, Q:F.87, N:T.408, N:W.409, X:F.9 Hydrogen bonds: Z:K.4 Water bridges: Z:A.6 Salt bridges: X:H.10 PGV.40: 22 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155, I.158 Chain P: H.9, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, F.93 Ligands: PGV.43, PEK.49 15 PLIP interactions: 9 interactions with chain P, 6 interactions with chain N Hydrophobic interactions: P:T.28, P:W.57, P:W.57, P:W.58, P:F.86, P:F.93, N:V.155, N:I.158 Hydrogen bonds: P:H.9, P:W.57, P:E.64, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.43: 20 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, F.86, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.40, CDL.44 26 PLIP interactions: 24 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:H.231, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.8: 14 residues within 4Å: Chain A: V.350, N.422, F.426, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:V.350, A:N.422, A:F.426, A:F.430, B:V.31, B:F.32, B:F.32, B:L.39 Salt bridges: B:H.24, I:R.43 TGL.22: 14 residues within 4Å: Chain A: I.332, W.334, M.339, K.411, F.414, A.415 Chain B: L.46, T.47, T.48 Chain D: R.73, E.77, W.78, V.81 Chain I: R.16 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.81, A:W.334, A:W.334, A:F.414 Water bridges: D:W.78 Salt bridges: A:K.411 TGL.28: 18 residues within 4Å: Chain A: F.2, L.7, T.17, L.21, F.22, W.25, F.393, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, R.20, M.25, F.28, F.29, S.31 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain L Hydrophobic interactions: A:L.21, A:F.22, A:F.22, A:W.25, A:F.393, A:I.472, L:I.11, L:F.13, L:F.28, L:F.28, L:F.29 TGL.35: 13 residues within 4Å: Chain N: W.334, M.339, K.411 Chain O: I.42, L.46 Chain Q: N.72, R.73, T.75, E.77, W.78, V.81 Chain V: R.16, H.20 9 PLIP interactions: 4 interactions with chain N, 3 interactions with chain Q, 2 interactions with chain O Hydrophobic interactions: N:W.334, N:W.334, N:K.411, Q:W.78, Q:V.81, O:I.42, O:L.46 Salt bridges: N:K.411 Hydrogen bonds: Q:W.78 TGL.51: 14 residues within 4Å: Chain N: V.350, N.422, F.426, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, F.32, S.35, L.39 Chain V: F.31, R.43 8 PLIP interactions: 3 interactions with chain O, 3 interactions with chain N, 2 interactions with chain V Hydrophobic interactions: O:L.28, O:F.32, N:V.350, N:F.426, N:F.430, V:F.31 Salt bridges: O:H.24, V:R.43 TGL.53: 16 residues within 4Å: Chain N: F.2, L.7, T.17, L.18, L.21, L.113, F.400, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29 14 PLIP interactions: 8 interactions with chain Y, 6 interactions with chain N Hydrophobic interactions: Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29, N:F.2, N:T.17, N:L.18, N:L.113, N:F.400, N:I.472

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.9: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) CMO.37: 7 residues within 4Å: Chain N: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.31, CU.32 No protein-ligand interaction detected (PLIP)

2 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.10: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204 CUA.39: 6 residues within 4Å: Chain O: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.196, O:E.198, O:C.200, O:C.200, O:H.204

2 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.11: 15 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: H.52, M.56, D.57, E.60, W.65 Chain E: D.8, F.11, L.41 Chain I: L.17, R.18, I.21, F.25 10 PLIP interactions: 3 interactions with chain B, 4 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: B:W.65, B:W.65, I:L.17, I:I.21, I:F.25, A:F.321, A:F.321, A:A.325 Hydrogen bonds: B:D.57 Salt bridges: I:R.18 PSC.47: 15 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, H.52, T.55, D.57, E.60, V.61, I.64 Chain R: H.5, E.6, T.7, D.8 Chain V: L.17 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: O:I.41, O:V.61, O:I.64, N:F.321 Salt bridges: R:D.8

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.12: 12 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 10 PLIP interactions: 3 interactions with chain T, 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: T:F.18, A:M.271, A:W.275, A:W.275, A:W.275 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:E.62, B:E.62, B:T.63 CHD.13: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Chain P: L.127 Ligands: PGV.16, CDL.50 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:W.288, A:Y.304 CHD.18: 6 residues within 4Å: Chain C: R.156, K.157, L.160, F.164, L.223 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:F.164, C:F.164, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.27: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:R.33, J:L.40 Hydrogen bonds: J:R.33 CHD.38: 13 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: Q.59, E.62, T.63, T.66 Ligands: PEK.20 13 PLIP interactions: 4 interactions with chain N, 6 interactions with chain G, 3 interactions with chain O Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, G:F.18, G:F.18 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:E.62, O:E.62, O:T.63 CHD.41: 8 residues within 4Å: Chain C: L.127 Chain N: H.233, D.300, T.301, Y.304 Chain P: W.99, H.103 Ligands: PGV.26 8 PLIP interactions: 6 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:T.301, N:Y.304 Hydrogen bonds: N:T.301, N:T.301, P:W.99 Water bridges: N:T.301 Salt bridges: N:H.233, P:H.103 CHD.45: 4 residues within 4Å: Chain P: R.156, Q.161, F.164 Chain W: F.1 3 PLIP interactions: 3 interactions with chain P Hydrophobic interactions: P:F.164, P:F.164 Salt bridges: P:R.156 CHD.52: 4 residues within 4Å: Chain W: Y.32, R.33, M.36, T.37 1 PLIP interactions: 1 interactions with chain W Hydrophobic interactions: W:R.33

6 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.14: 20 residues within 4Å: Chain A: H.151, L.210, L.215 Chain C: F.35, T.174, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 15 PLIP interactions: 7 interactions with chain G, 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: G:W.62, G:F.69, C:F.35, C:T.174, C:Y.181, C:F.203, C:F.203, A:L.210, A:L.215 Hydrogen bonds: G:T.68, G:F.69, G:F.70, G:N.76, G:N.76, C:I.188 PEK.20: 13 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, Y.172 Chain G: R.17, F.21, G.22 Chain N: S.279 Chain O: Q.59, T.66 Ligands: CDL.24, CHD.38 9 PLIP interactions: 2 interactions with chain O, 4 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: O:T.66, C:T.168, C:Y.172, G:F.21 Hydrogen bonds: O:Q.59, C:K.157, C:H.158 Water bridges: G:R.17 Salt bridges: G:R.17 PEK.21: 15 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, V.91, T.95, F.98, W.240, F.244, V.247, F.251 Chain T: A.3, H.8, T.11 Ligands: PGV.16 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain T Hydrophobic interactions: C:I.84, C:V.91, C:F.98, C:W.240, C:W.240, C:F.251, C:F.251, T:A.3 Hydrogen bonds: C:K.77, C:Y.81, T:H.8 Salt bridges: C:R.80 PEK.25: 15 residues within 4Å: Chain G: A.3, G.6, T.11, W.16 Chain P: R.80, I.84, L.85, V.91, F.98, E.236, W.240, H.243, V.247, F.251 Ligands: CDL.24 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain G Hydrophobic interactions: P:L.85, P:V.91, P:F.98, P:F.98, P:H.243, P:V.247, P:F.251, P:F.251, P:F.251, G:A.3, G:W.16 Hydrogen bonds: P:E.236 PEK.42: 12 residues within 4Å: Chain A: W.275 Chain B: Q.59, T.66, I.67 Chain P: H.158, Q.161, L.175 Chain T: R.17, F.21, L.23, L.30 Ligands: CDL.50 10 PLIP interactions: 5 interactions with chain T, 2 interactions with chain B, 2 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: T:F.21, T:F.21, T:L.23, T:L.30, B:T.66, B:I.67, P:L.175, A:W.275 Salt bridges: T:R.17 Hydrogen bonds: P:H.158 PEK.49: 21 residues within 4Å: Chain N: H.151, T.207 Chain P: L.31, W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, L.206 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.40 15 PLIP interactions: 8 interactions with chain T, 7 interactions with chain P Hydrophobic interactions: T:W.62, T:F.69, T:F.69, P:L.31, P:W.34, P:Y.181, P:F.203, P:L.206 Hydrogen bonds: T:T.68, T:F.69, T:F.70, T:N.76, T:N.76, P:A.184, P:I.188

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 19 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, R.59, I.62, R.63, F.67, T.213, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27, D.28 Ligands: PGV.15 14 PLIP interactions: 2 interactions with chain J, 12 interactions with chain C Hydrophobic interactions: J:T.27, C:M.51, C:L.52, C:Y.55, C:I.62, C:V.217 Water bridges: J:D.28, C:R.59 Hydrogen bonds: C:Y.55, C:R.63 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226 CDL.24: 24 residues within 4Å: Chain C: N.125, L.127, L.131, L.138, F.251 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Chain N: F.282, D.300, Y.304, S.307, I.311 Chain O: A.77, L.78, L.81, Y.85 Ligands: PEK.20, PEK.25, PGV.26 12 PLIP interactions: 3 interactions with chain O, 3 interactions with chain C, 4 interactions with chain G, 2 interactions with chain N Hydrophobic interactions: O:A.77, O:L.78, O:L.81, C:L.138, C:F.251, G:L.23, G:L.30, G:L.37, N:F.282, N:Y.304 Hydrogen bonds: C:N.125 Salt bridges: G:H.38 CDL.44: 19 residues within 4Å: Chain P: M.51, Y.55, W.58, R.59, I.62, R.63, F.67, T.174, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain W: K.8, F.12, T.27 Ligands: PGV.43 18 PLIP interactions: 17 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:M.51, P:Y.55, P:W.58, P:I.62, P:T.174, P:T.213, P:I.216, P:V.217, P:F.220, P:F.220 Hydrogen bonds: P:Y.55, P:R.63 Salt bridges: P:R.63, P:K.224, P:K.224, P:K.224, P:H.226, W:K.8 CDL.50: 22 residues within 4Å: Chain A: F.282, D.300, Y.304, S.307, I.311 Chain B: L.78, L.81, Y.85 Chain P: L.127, L.131, T.134, L.138, L.250, W.258 Chain T: A.1, S.27, C.31, N.34, L.37, H.38 Ligands: CHD.13, PEK.42 14 PLIP interactions: 4 interactions with chain A, 2 interactions with chain T, 5 interactions with chain P, 3 interactions with chain B Hydrophobic interactions: A:F.282, A:F.282, A:Y.304, A:I.311, T:A.1, P:L.131, P:T.134, P:L.138, P:L.250, P:W.258, B:L.78, B:L.81 Salt bridges: T:H.38 Water bridges: B:R.82

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.19: 5 residues within 4Å: Chain C: N.38, M.40 Chain G: W.62, G.63, F.69 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:F.69 Hydrogen bonds: G:G.63, C:N.38, C:M.40 DMU.29: 10 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 9 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, 2 interactions with chain M Hydrophobic interactions: D:L.95, D:W.98, D:W.98, D:W.98, A:L.35, A:F.459, A:F.459, M:L.27 Hydrogen bonds: M:Y.35 DMU.46: 3 residues within 4Å: Chain P: M.40 Chain T: W.62, G.63 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.63 DMU.54: 13 residues within 4Å: Chain N: L.35, F.459, L.462 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 8 PLIP interactions: 3 interactions with chain Z, 3 interactions with chain Q, 2 interactions with chain N Hydrophobic interactions: Z:L.27, Z:L.34, Q:L.95, Q:W.98, Q:W.98, N:L.35, N:L.462 Hydrogen bonds: Z:W.32

2 x ZN: ZINC ION(Non-covalent)

ZN.23: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85 ZN.48: 5 residues within 4Å: Chain S: C.60, C.62, C.82, C.85, T.87 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishigami, I. et al., Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-09

Peptides

Cytochrome c oxidase subunit 1: AN
Cytochrome c oxidase subunit 2: BO
Cytochrome c oxidase subunit 3: CP
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: DQ
Cytochrome c oxidase subunit 5A, mitochondrial: ER
Cytochrome c oxidase subunit 5B, mitochondrial: FS
Cytochrome c oxidase subunit 6A2, mitochondrial: GT
Cytochrome c oxidase subunit 6B1: HU
Cytochrome c oxidase subunit 6C: IV
Cytochrome c oxidase subunit 7A1, mitochondrial: JW
Cytochrome c oxidase subunit 7B, mitochondrial: KX
Cytochrome c oxidase subunit 7C, mitochondrial: LY
Cytochrome c oxidase subunit 8B, mitochondrial: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
a

B
B

O
b

C
C

P
c

D
D

Q
d

E
E

R
e

F
F

S
f

G
G

T
g

H
H

U
h

I
I

V
i

J
J

W
j

K
K

X
k

L
L

Y
l

M
M

Z
m

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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